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Molecular evolution of synonymous codon usage in Populus
Umeå University, Faculty of Science and Technology, Ecology and Environmental Science.
2008 (English)In: BMC Evol Biol, ISSN 1471-2148, Vol. 8, 307- p.Article in journal (Refereed) Published
Abstract [en]

Background Evolution of synonymous codon usage is thought to be determined by a balance between mutation, genetic drift andnatural selection on translational efficiency. However, natural selection on codon usage is considered to be a weak evolutionary force and selection on codon usage is expected to be strongest in species with large effective population sizes. Results I examined the evolution of synonymous codons using EST data from five species of Populus. Data on relative synonymous codon usage in genes with high and low gene expression were used to identify 25 codons from 18 different amino acids that were deemed to be preferred codons across all five species.All five species show significant correlations between codon bias and gene expression, independent of base composition, thus indicating that translational selection has shaped synonymous codon usage. Using a set of 158 orthologous genes I detected an excess of unpreferred to preferred (U->P) mutations in two lineages, P. tremula and P. deltoides. Maximum likelihood estimates of the strength of selection acting on synonymous codons was also significantly greater than zero in P. tremula, with the ML estimate of 4N[es]=0.720. Conclusions The data is consistent with weak selection on preferred codons in all five species. There is also evidence suggesting that selection on synonymous codons has increased in P. tremula. Although the reasons for the increase in selection on codon usage in the P. tremula lineage are not clear, one possible explanation is an increase in the effective population size in P. tremula.

Place, publisher, year, edition, pages
2008. Vol. 8, 307- p.
Keyword [en]
Base Composition, Codon, Computational Biology, DNA; Plant/genetics, Evolution; Molecular, Expressed Sequence Tags, Gene Expression, Gene Expression Profiling, Genetics; Population, Genome; Plant, Likelihood Functions, Models; Genetic, Mutation, Phylogeny, Polymorphism; Genetic, Populus/*genetics, Selection (Genetics), Sequence Alignment, Sequence Analysis; DNA
URN: urn:nbn:se:umu:diva-11350DOI: doi:10.1186/1471-2148-8-307PubMedID: 18983655OAI: diva2:151021
Available from: 2008-12-16 Created: 2008-12-16 Last updated: 2011-01-10Bibliographically approved

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Ingvarsson, Pär
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